diff --git a/.test/configs/project.ped b/.test/configs/project_1_sample.ped
similarity index 57%
rename from .test/configs/project.ped
rename to .test/configs/project_1_sample.ped
index a17d4e13c9a5a6912f320ea3dc18a1b026546c96..41e547acb61a420b9529b9fd2ad2866df20e6f29 100644
--- a/.test/configs/project.ped
+++ b/.test/configs/project_1_sample.ped
@@ -1,3 +1,2 @@
#family_id sample_id paternal_id maternal_id sex phenotype
-unknown A -9 -9 -9 -9
-unknown B -9 -9 -9 -9
+unknown A father_1 mother_1 -9 -9
diff --git a/.test/configs/project_2_samples.ped b/.test/configs/project_2_samples.ped
new file mode 100644
index 0000000000000000000000000000000000000000..91a691c58614b76172379e78a4c31c38e8bfef2d
--- /dev/null
+++ b/.test/configs/project_2_samples.ped
@@ -0,0 +1,3 @@
+#family_id sample_id paternal_id maternal_id sex phenotype
+unknown A father_1 mother_1 -9 -9
+unknown B father_1 mother_1 -9 -9
diff --git a/Changelog.md b/Changelog.md
index 6571dec1d93b44530a0e84c4257dfa41c4d325cd..3d0fccc05287590dc545ef1239f6238c8b8c57be 100644
--- a/Changelog.md
+++ b/Changelog.md
@@ -30,3 +30,8 @@ YYYY-MM-DD John Doe
* QuaC's input are output from the small variant caller pipeline, and former's output will fit seemlessly with the latter's output.
* QuaC accepts pedigree file as input. A dummy pedigree file creator script is provided, which will be handy until phenotips is made available to us.
* System-level testing is added
+
+2021-06-08 Manavalan Gajapathy
+
+* Bugfix: Fixes error when there is only one sample in input ped file (#34)
+* Adds system-testing for such only-one-sample-in-input setup (#35).
diff --git a/README.md b/README.md
index 126ab3f84be6893ddb322be3029cb526d1be4f27..67047b5d018fdf8cb598a45c52a28015f2828035 100644
--- a/README.md
+++ b/README.md
@@ -318,7 +318,7 @@ conda activate quac
python src/run_quac.py \
--project_name test_project \
--projects_path ".test/ngs-data/" \
- --pedigree ".test/configs/project.ped" \
+ --pedigree ".test/configs/project_2_samples.ped" \
--outdir "$USER_SCRATCH/tmp/quac/results/test_project_wgs/analysis" \
-e="--conda-create-envs-only"
```
@@ -402,27 +402,30 @@ module load Anaconda3/2020.02
conda activate quac
# WGS mode
+PROJECT="project_2_samples"
python src/run_quac.py \
--project_name test_project \
--projects_path ".test/ngs-data/" \
- --pedigree ".test/configs/project.ped" \
- --outdir "$USER_SCRATCH/tmp/quac/results/test_project_wgs/analysis"
+ --pedigree ".test/configs/${PROJECT}.ped" \
+ --outdir "$USER_SCRATCH/tmp/quac/results/test_${PROJECT}_wgs/analysis"
# Exome mode
python src/run_quac.py \
--project_name test_project \
--projects_path ".test/ngs-data/" \
- --pedigree ".test/configs/project.ped" \
- --outdir "$USER_SCRATCH/tmp/quac/results/test_project_exome/analysis" \
+ --pedigree ".test/configs/${PROJECT}.ped" \
+ --outdir "$USER_SCRATCH/tmp/quac/results/test_${PROJECT}_exome/analysis" \
--quac_watch_config "configs/quac_watch/exome_quac_watch_config.yaml" \
--exome
```
+Note: Use `PROJECT="project_1_sample"` to test out a project with only one sample.
+
### Expected output files
```sh
-$ tree $USER_SCRATCH/tmp/quac/results/test_project/ -d -L 4
-/data/scratch/manag/tmp/quac/results/test_project/
+$ tree $USER_SCRATCH/tmp/quac/results/test_project_2_samples/ -d -L 4
+/data/scratch/manag/tmp/quac/results/test_project_2_samples/
└── analysis
├── A
│  └── qc
@@ -494,14 +497,14 @@ DAG_DIR="pipeline_visualized"
python src/run_quac.py \
--project_name test_project \
--projects_path .test/ngs-data/ \
- --pedigree .test/configs/project.ped \
+ --pedigree .test/configs/project_2_samples.ped \
--run_locally --extra_args "--dag -F | dot -Tpng > ${DAG_DIR}/wgs_dag.png"
# Rulegraph - less informative than DAG at sample level but less dense than DAG makes this easier to skim
python src/run_quac.py \
--project_name test_project \
--projects_path .test/ngs-data/ \
- --pedigree .test/configs/project.ped \
+ --pedigree .test/configs/project_2_samples.ped \
--run_locally --extra_args "--rulegraph -F | dot -Tpng > ${DAG_DIR}/wgs_rulegraph.png"
###### Exome mode ######
@@ -509,7 +512,7 @@ python src/run_quac.py \
python src/run_quac.py \
--project_name test_project \
--projects_path .test/ngs-data/ \
- --pedigree .test/configs/project.ped \
+ --pedigree .test/configs/project_2_samples.ped \
--exome \
--quac_watch_config "configs/quac_watch/exome_quac_watch_config.yaml" \
--run_locally --extra_args "--dag -F | dot -Tpng > ${DAG_DIR}/exome_dag.png"
@@ -518,7 +521,7 @@ python src/run_quac.py \
python src/run_quac.py \
--project_name test_project \
--projects_path .test/ngs-data/ \
- --pedigree .test/configs/project.ped \
+ --pedigree .test/configs/project_2_samples.ped \
--exome \
--quac_watch_config "configs/quac_watch/exome_quac_watch_config.yaml" \
--run_locally --extra_args "--rulegraph -F | dot -Tpng > ${DAG_DIR}/exome_rulegraph.png"
diff --git a/workflow/rules/coverage_analysis.smk b/workflow/rules/coverage_analysis.smk
index 872357a58f67cbb33f11abd78f6d9535ec9d6de0..e8ff6198094ea24176122b5f703167d415dd27a1 100644
--- a/workflow/rules/coverage_analysis.smk
+++ b/workflow/rules/coverage_analysis.smk
@@ -124,13 +124,11 @@ rule mosdepth_plot:
protected(OUT_DIR / "project_level_qc" / "mosdepth" / "mosdepth.html"),
message:
"Running mosdepth plotting"
- params:
- infiles=lambda wildcards: str(OUT_DIR / f"{{{','.join(SAMPLES)}}}" / "qc" / "mosdepth" / "*.mosdepth.global.dist.txt"),
shell:
r"""
python {input.script} \
--output {output} \
- {params.infiles}
+ {input.dist}
"""
@@ -156,12 +154,11 @@ rule indexcov:
str(WORKFLOW_PATH / "configs/env/goleft.yaml")
params:
outdir=lambda wildcards, output: Path(output[0]).parent,
- infiles=lambda wildcards: str(PROJECT_PATH / f"{{{','.join(SAMPLES)}}}" / "bam" / "*.bam"),
shell:
r"""
goleft indexcov \
--directory {params.outdir} \
- {params.infiles} \
+ {input.bam} \
> {log} 2>&1
"""
diff --git a/workflow/rules/relatedness_ancestry.smk b/workflow/rules/relatedness_ancestry.smk
index 4c37b6880a3483ce24384e42b0a333f0deef4393..5bacedf72820debb755c49e871948b75e246b201 100644
--- a/workflow/rules/relatedness_ancestry.smk
+++ b/workflow/rules/relatedness_ancestry.smk
@@ -41,14 +41,13 @@ rule somalier_relate:
log=OUT_DIR / "project_level_qc" / "somalier" / "relatedness" / "somalier.log",
params:
outdir=lambda wildcards, output: Path(output["out"][0]).parent,
- infiles=lambda wildcards: str(OUT_DIR / "project_level_qc" / "somalier" / "extract" / f"{{{','.join(SAMPLES)}}}.somalier"),
shell:
r"""
somalier relate \
--ped {input.ped} \
--infer \
--output-prefix {params.outdir}/somalier \
- {params.infiles} \
+ {input.extracted} \
> {log} 2>&1
"""
@@ -73,13 +72,12 @@ rule somalier_ancestry:
log=OUT_DIR / "project_level_qc" / "somalier" / "ancestry" / "somalier.log",
params:
outdir=lambda wildcards, output: Path(output["out"][0]).parent,
- infiles=lambda wildcards: str(OUT_DIR / "project_level_qc" / "somalier" / "extract" / f"{{{','.join(SAMPLES)}}}.somalier"),
shell:
r"""
somalier ancestry \
--output-prefix {params.outdir}/somalier \
--labels {input.labels_1kg} \
{input.somalier_1kg_directory}/*.somalier ++ \
- {params.infiles} \
+ {input.extracted} \
> {log} 2>&1
"""